A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/diseasemodulediscovery analysis pipeline. For information about how to interpret these results, please see the documentation.
/home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/work/51/e7fabed3b5dcd31e2f36d85ba16c20
General Statistics
| Sample Name | Nodes | Edges | Seeds | Diameter | Components | Largest component | Max distance to seed | Isolated nodes | Robustness (seeds permutation) | Seed rediscovery | Seed rediscovery (normalized) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.diamond | 215 | 1321 | 15 | 5 | 11 | 204 | 3 | 8 | 0.86 | 0.00 | 0.0000 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.domino | 13 | 12 | 5 | 2 | 3 | 8 | 1 | 0 | 0.89 | 0.07 | 0.0074 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor | 1004 | 4218 | 15 | 7 | 2 | 1002 | 1 | 0 | 0.94 | 0.13 | 0.0001 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.no_tool | 15 | 5 | 15 | 0 | 14 | 2 | 0 | 9 | |||
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust | 70 | 97 | 15 | 8 | 3 | 64 | 2 | 0 | 0.89 | 0.07 | 0.0012 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust_bias_aware | 74 | 97 | 15 | 11 | 1 | 74 | 3 | 0 | 0.89 | 0.07 | 0.0012 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.rwr | 104 | 236 | 15 | 9 | 1 | 104 | 2 | 0 | 0.91 | 0.13 | 0.0015 |
WARNING: Modules not visualized
List of modules with too many nodes for visualization. The maximum number of nodes can be adjusted with the '--visualization_max_nodes' parameter.
| Module | Nodes |
|---|---|
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor | 1004 |
WARNING: Modules too large for Drugst.One
List of modules with too many nodes for Drugst.One export and drug prioritization. The maximum number of nodes can be adjusted with the '--drugstone_max_nodes' parameter.
| Module | Nodes |
|---|---|
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.firstneighbor | 1004 |
Input
Shows the number of seeds retained from the input files and the number of seeds removed (not in network)..
Network
| Network | Nodes | Edges | Diameter | Components | Largest component | Self loops | Duplicate edges |
|---|---|---|---|---|---|---|---|
| filtered_ppi_only_reviewed_proteins_solution | 12797 | 95916 | 10 | 101 | 12651 | 1175 | 0 |
Seeds
Drugstone Links
Using the links in this table you can see the modules visualized with the Drugst.One API.
| Module_id | drugstone_link | link_raw |
|---|---|---|
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.diamond | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.diamond | https://drugst.one/?id=4ff75484b0b946289091f61f7f6cf7a4 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.domino | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.domino | https://drugst.one/?id=a8463ffcd07f40de85ed408251035072 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.no_tool | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.no_tool | https://drugst.one/?id=eb16d1e81031485d8c557ac307f506a8 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust | https://drugst.one/?id=293ec0b752dd4182846ab4b592a27693 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust_bias_aware | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.robust_bias_aware | https://drugst.one/?id=b4b3a571a1e54e26b057eab3500694a8 |
| seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.rwr | seed_genes_huntingtons_disease.filtered_ppi_only_reviewed_proteins_solution.rwr | https://drugst.one/?id=92bd4bd4f33c401aae8ac778822cff60 |
Overlap
Jaccard similarity between the gene sets of the modules, excluding the seeds.
Jaccard similarity
Jaccard similarity (without seeds)
Shared nodes
Shared nodes (without seeds)
Robustness (seeds permutation)
Jaccard index distributions between the original and permuted modules.
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| BIOPAX_PARSER | graph-tool | 2.77 (commit 4ad25c62, ) |
| nedrex | 0.1.4 | |
| pybiopax | 0.1.4 | |
| python | 3.12.7 | |
| BIOPAX_VALIDATOR | biopax-validator | /biopax-validator/lib/biopax-validator-6.0.0-SNAPSHOT.jar |
| java | openjdk version "20.0.2.1" 2023-08-22 | |
| DIAMOND | python | 3.8.5 |
| DOMINO_DOMINO | python | 3.6.15 |
| DOMINO_SLICER | python | 3.6.15 |
| DRUGPREDICTIONS | drugstone | 0.4.5 |
| pandas | 2.2.3 | |
| python | 3.12.7 | |
| DRUGSTONEEXPORT | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| FIRSTNEIGHBOR | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| GPROFILER2_GOST | r-ggplot2 | 3.4.3 |
| r-gprofiler2 | 0.2.2 | |
| GRAPHTOOLPARSER | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| MODULEPARSER | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| NETWORKANNOTATION | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| ROBUST | python | 3.10.4 |
| ROBUSTBIASAWARE | python | 3.10.14 |
| robust-bias-aware | 0.0.1 | |
| RWR | python | 3.12.7 |
| SAVEMODULES | graph-tool | 2.77 (commit 4ad25c62, ) |
| pandas | 2.2.3 | |
| python | 3.12.7 | |
| SEEDPERMUTATION | python | 3.12.7 |
| SEEDPERMUTATIONEVALUATION | python | 3.12.7 |
| TOPOLOGY | graph-tool | 2.77 (commit 4ad25c62, ) |
| python | 3.12.7 | |
| VISUALIZEMODULES | graph-tool | 2.77 (commit 4ad25c62, ) |
| networkx | 3.3 | |
| pyintergraph | 1.3.3 | |
| python | 3.12.7 | |
| pyvis | 0.3.1 | |
| VISUALIZEMODULESDRUGS | graph-tool | 2.77 (commit 4ad25c62, ) |
| networkx | 3.3 | |
| pyintergraph | 1.3.3 | |
| python | 3.12.7 | |
| pyvis | 0.3.1 | |
| Workflow | Nextflow | 24.10.5 |
| nf-core/diseasemodulediscovery | v1.0dev-g8cec67b |
nf-core/diseasemodulediscovery Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/diseasemodulediscovery
Methods
Data was processed using nf-core/diseasemodulediscovery v1.0dev of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v24.10.5 (Di Tommaso et al., 2017) with the following command:
nextflow run nf-core/diseasemodulediscovery -r dev -profile docker --seeds ../data/NeDRex_api/seed_genes_huntingtons_disease.csv --network ../data/NeDRex_api/filtered_ppi_only_reviewed_proteins_solution.csv --id_space uniprot --skip_digest --outdir results --run_seed_permutation -resume
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
Notes:
- If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/diseasemodulediscovery Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/diseasemodulediscovery
Input/output options
- id_space
- uniprot
- network
- ../data/NeDRex_api/filtered_ppi_only_reviewed_proteins_solution.csv
- outdir
- results
- seeds
- ../data/NeDRex_api/seed_genes_huntingtons_disease.csv
Module evaluation
- run_seed_permutation
- true
- skip_digest
- true
Generic options
- trace_report_suffix
- 2025-08-19_16-54-30
Core Nextflow options
- configFiles
- /home/johannes/.nextflow/assets/nf-core/diseasemodulediscovery/nextflow.config, /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/nextflow.config
- container
- ghcr.io/repo4eu/modulediscovery_python_dependencies:v0.1.0
- containerEngine
- docker
- launchDir
- /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline
- profile
- docker
- projectDir
- /home/johannes/.nextflow/assets/nf-core/diseasemodulediscovery
- revision
- dev
- runName
- shrivelled_lagrange
- userName
- johannes
- workDir
- /home/johannes/workspace/network_medicine_drug_repurposing_tutorial/nextflow_pipeline/work